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At least 145 records · Page 8

A chemical kinetics theory for interpreting the non-monotonic temperature dependence of enzymatic reactions

Abstract. One notable observation of enzymatic chemical reactions is that, for a given abundance of enzymes and substrates, temperature increases cause reaction rates to first increase consistent with the Arrhenius relationship, then plateau, and finally fall off quickly to zero at high temperatures. While many mathematical functions have been used to describe this pattern, we here propose a chemical kinetics theory which successfully replicates this observation and provides insights into the processes responsible for these dynamics. The chemical kinetics theory combines the law of mass action, von Smoluchowski's diffusion-limited chemical reaction theory, and Eyring's transition state theory. This new theory reveals that the thermally reversible enzyme denaturation ensured by the ceaseless thermal motion of molecules and ions in an enzyme solution explains the plateau and subsequent decrease in chemical reaction rates with increasing temperature. The temperature-dependent affinity parameter (K) that relates enzymes and substrates through their binding also affects the shape of the emergent temperature response. We demonstrate that with an increase in substrate availability, K shifts the optimal temperature, where reaction rates plateau, towards higher values. Further, we show that the chemical kinetics theory accurately represents 12 sets of published enzyme assay data and includes the popular mechanistic model by Ratkowsky et al. (2005) as a special case. Given its good performance and solid theoretical underpinning, we believe this new theory will facilitate the construction of more mechanistic-based environmental biogeochemical models.

Tang, Jinyun↗

Interacting fractons in 2+1-dimensional quantum field theory

We analyze, in perturbation theory, a theory of weakly interacting fractons and non-relativistic fermions in a 2+1 dimensional Quantum Field Theory. In particular we compute the 1-loop corrections to the self energies and interaction vertex, and calculate the associated 1-loop Renormalization Group flows of the coupling constants. Surprisingly, we find that the fracton-fermion coupling does not flow due to an emergent coordinate-dependent symmetry of the effective Lagrangian, making this model a well-defined quantum field theory. We provide additional discussions on the regularization and renormalization of interacting fractonic theories, as well as both qualitative and quantitative remarks regarding the theory at finite temperature and finite chemical potential.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Normalization of ZZ instanton amplitudes in minimal string theory

We use insights from string field theory to analyze and cure the divergences in the cylinder diagram in minimal string theory with both boundaries lying on a ZZ brane. We focus on theories with worldsheet matter consisting of the (2, p) minimal model plus Liouville theory, with total central charge 26, together with the usual bc-ghosts. The string field theory procedure gives a finite, purely imaginary normalization constant for non-perturbative effects in minimal string theory, or doubly non-perturbative effects in JT gravity. We find precise agreement with the prediction from the dual double-scaled one-matrix integral. We also make a few remarks about the extension of this result to the more general (p', p) minimal string.

2D gravity↗

A generalized Boltzmann kinetic theory for strongly magnetized plasmas with application to friction

Coulomb collisions in plasmas are typically modeled using the Boltzmann collision operator, or its variants, which apply to weakly magnetized plasmas in which the typical gyroradius of particles significantly exceeds the Debye length. Conversely, O’Neil has developed a kinetic theory to treat plasmas that are so strongly magnetized that the typical gyroradius of particles is much smaller than the distance of the closest approach in a binary collision. Here, we develop a generalized collision operator that applies across the full range of magnetization strength. Since there is no closed-form solution for the scattering cross section when plasma is strongly magnetized, the input to the collision operator is obtained by numerically calculating particle trajectories. To demonstrate novel physics associated with strong magnetization, it is used to compute the friction force on a massive test charge. In addition to the traditional stopping power component, this is found to exhibit a transverse component that is perpendicular to both the velocity and Lorentz force vectors in the strongly magnetized regime, as was predicted recently using linear response theory. As a result, good agreement is found between the collision theory and linear response theory in the regime in which both apply, but the new collision theory also applies to stronger magnetization strength regimes than the linear response theory is expected to apply in.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A new “gold standard”: Perturbative triples corrections in unitary coupled cluster theory and prospects for quantum computing

A major difficulty in quantum simulation is the adequate treatment of a large collection of entangled particles, synonymous with electron correlation in electronic structure theory, with coupled cluster (CC) theory being the leading framework for dealing with this problem. Augmenting computationally affordable low-rank approximations in CC theory with a perturbative account of higher-rank excitations is a tractable and effective way of accounting for the missing electron correlation in those approximations. This is perhaps best exemplified by the “gold standard” CCSD(T) method, which bolsters the baseline CCSD with the effects of triple excitations using considerations from many-body perturbation theory (MBPT). Despite this established success, such a synergy between MBPT and the unitary analog of CC theory (UCC) has not been explored. In this work, we propose a similar approach wherein converged UCCSD amplitudes are leveraged to evaluate energy corrections associated with triple excitations, leading to the UCCSD[T] method. In terms of quantum computing, this correction represents an entirely classical post-processing step that improves the energy estimate by accounting for triple excitation effects without necessitating new quantum algorithm developments or increasing demand for quantum resources. The rationale behind this choice is shown to be rigorous by studying the properties of finite-order UCC energy functionals, and our efforts do not support the addition of the fifth-order contributions as in the (T) correction. We assess the performance of these approaches on a collection of small molecules and demonstrate the benefits of harnessing the inherent synergy between MBPT and UCC theories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thermal mean-field theories

Several closely related ab initio thermal mean-field theories for fermions, both well-established and new ones, are compared with one another at the formalism level and numerically. The theories considered are Fermi–Dirac theory; thermal Hartree–Fock (HF) theory; two modifications of the thermal single-determinant and the first-order finite-temperature many-body perturbation theory based on a zero-temperature or thermal HF reference. Furthermore, thermal full-configuration-interaction theory is used as the benchmark.

74 ATOMIC AND MOLECULAR PHYSICS↗

Quantitative Predictive Theories through Integrating Quantum, Statistical, Equilibrium, and Nonequilibrium Thermodynamics

Today's thermodynamics is largely based on the combined law for equilibrium systems and statistical mechanics derived by Gibbs in 1873 and 1901, respectively, while irreversible thermodynamics for nonequilibrium systems resides essentially on the Onsager Theorem as a separate branch of thermodynamics developed in 1930s. Between them, quantum mechanics was invented and was quantitatively solved in terms of density functional theory (DFT) in 1960s. Furthermore, these three scientific domains operate based on different principles and are very much separated from each other. In analogy to the parable of the blind men and the elephant articulated by Perdew, they individually represent different portions of a complex system and thus are incomplete by themselves alone, resulting in the lack of quantitative agreement between their predictions and experimental observations. Over the last two decades, the author's group has developed a multiscale entropy approach (recently termed as zentropy theory) that integrates DFT-based quantum mechanics and Gibbs statistical mechanics and is capable of accurately predicting entropy and free energy of complex systems. Furthermore, in combination with the combined law for nonequilibrium systems developed by Hillert, the author developed the theory of cross phenomena beyond the phenomenological Onsager Theorem. The zentropy theory and theory of cross phenomena jointly provide quantitative predictive theories for systems from electronic to any observable scales as reviewed in the present work.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Sensitivity of time-dependent density functional theory to initial conditions

Time-dependent density-functional theory is mathematically formulated through nonlinear coupled time-dependent three-dimensional partial differential equations, and it is natural to expect a strong sensitivity of its solutions to variations of the initial conditions, akin to the butterfly effect ubiquitous in classical dynamics. Since the Schrödinger equation for an interacting many-body system is, however, linear and mathematically the exact equations of the density-functional theory reproduce the corresponding one-body properties, it would follow that the Lyapunov exponents are also vanishing within a density-functional theory framework. Whether for realistic implementations of the time-dependent density-functional theory the question of the absence of the butterfly effect and whether the dynamics provided is indeed a predictable theory was never discussed. At the same time, since the time-dependent density-functional theory is a unique tool allowing us to study the nonequilibrium dynamics of strongly interacting many-fermion systems, the question of predictability of this theoretical framework is of paramount importance. Here our analysis, for a number of quantum superfluid many-body systems (unitary Fermi gas, nuclear fission, and heavy-ion collisions) with a classical equivalent number of degrees of freedom O(10 10 ) and larger, suggests that its maximum Lyapunov exponents are negligible for all practical purposes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Phases of Theories with ℤ 𝑁 1-Form Symmetry, and the Roles of Center Vortices and Magnetic Monopoles

We analyze the phases of theories having a microscopic ℤ 𝑁 1-form symmetry, starting with a topological BF theory and deforming it so that only the microscopic symmetry is preserved. These theories have a well-defined notion of confinement, prototypical examples being pure SU⁡(𝑁) and ℤ 𝑁 gauge theories in the continuum and on the lattice. Our analysis shows that the generic phases are in 𝑑 = 2, only the confined phase; in 𝑑 = 3, both the confined phase and the topological BF phase; and in 𝑑 = 4, the confined phase, the topological BF phase, and a Coulomb phase. We construct a ℤ𝑁 lattice gauge theory with a deformation that, surprisingly, produces up to (𝑁−1) photons. We give an interpretation of these findings in terms of the behaviors of two competing drivers of confinement—magnetic monopoles and center vortices—and conclude that proliferation of center vortices is necessary but insufficient for confinement, while proliferation of magnetic monopoles is both necessary and sufficient.

Color confinement↗

Detectors in weakly-coupled field theories

We initiate a study of asymptotic detector operators in weakly-coupled field theories. These operators describe measurements that can be performed at future null infinity in a collider experiment. In a conformal theory they can be identified with light-ray operators, and thus have a direct relation to the spectrum of the theory. After a general discussion of the underlying physical picture, we show how infrared divergences of general detector operators can be renormalized in perturbation theory, and how they give rise to detector anomalous dimensions. We discuss in detail how this renormalization can be performed at the intersections of the Regge trajectories where non-trivial mixing occurs, which is related to the poles in anomalous dimensions at special values of spin. Finally, we discuss novel horizontal trajectories in scalar theories and show how they contribute to correlation functions. Our calculations are done in the example of Φ 4 theory in d = 4 - ϵ dimensions, but the methods are applicable more broadly. At the Wilson-Fisher fixed point our results include an explicit expression for the Pomeron light-ray operator at two loops, as well as a prediction for the value of the Regge intercept at five loops.

47 OTHER INSTRUMENTATION↗

Effective Field Theory for the perturbations of a slowly rotating black hole

We develop the effective theory for perturbations around black holes with scalar hair, in two directions. First, we show that the scalar-Gauss-Bonnet theory, often used as an example exhibiting scalar black hole hair, can be deformed by galileon operators leading to order unity changes to its predictions. The effective theory for perturbations thus provides an efficient framework for describing and constraining broad classes of scalar-tensor theories, of which the addition of galileon operators is an example. Second, we extend the effective theory to perturbations around an axisymmetric, slowly rotating black hole, at linear order in the black hole spin. We also discuss the inclusion of parity-breaking operators in the effective theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Cauchy data space and multisymplectic formulation of conformal classical field theories

In this article we inspect the dynamics of classical field theories with a local conformal behavior. Our interest in the multisymplectic setting comes from its suitable description of field theories, and the conformal character has been added to account for field theories that are scale invariant, flat spaces, and because some conformal fields can be exactly solved or classified. In particular, we will solve the example of a conformal scalar field using the geometric Hamilton–Jacobi theory that is explicitly proposed for conformal fields on a multisymplectic manifold. To complete the geometric approach to study field theories, we propose the Hamilton–Jacobi theory for conformal fields in a Cauchy data space, in which space and time are split separately and the dynamics is depicted in an infinite-dimensional manifold.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Metal-to-Ligand Charge-Transfer Spectrum of a Ru-Bipyridine-Sensitized TiO 2 Cluster from Embedded Multiconfigurational Excited-State Theory

Understanding optical properties of the dye molecule in dye-sensitized solar cells (DSSCs) from first-principles quantum mechanics can contribute to improving the efficiency of such devices. While density functional theory (DFT) and time-dependent DFT have been pivotal in simulating optoelectronic properties of photoanodes used in DSSCs at the atomic scale, questions remain regarding DFT’s adequacy and accuracy to furnish critical information needed to understand the various excited-state processes involved. In this work, we simulate the absorption spectra of a dye-sensitized solar cell analogue, comprised of a Ru-bipyridine (Ru-bpy) dye molecule and a small TiO2 cluster via DFT and via an accurate embedded correlated wavefunction (CW) theory. We generated CW spectra for the adsorbed Ru-bpy dye via a recently introduced capped density functional embedding theory or capped-DFET (to generate the embedding potential that accounts for the interaction of the molecule and the TiO 2 cluster). We then combined capped-DFET with the accurate but expensive multiconfigurational complete active space second-order perturbation theory (CASPT2)—embedded CASPT2. Because the CW theory is conducted on only a portion of the total system in the presence of an embedding potential that describes that portion’s interaction with its environment, we efficiently obtain CW-quality predictions that reflect local properties of the entire system. Specifically, for example, with capped-DFET and embedded CW theory, we can simulate accurately a plethora of metal-to-ligand charge-transfer excited properties at a manageable computational cost. Here, we predict detailed electronic spectra within the visible region, featuring the lowest three singlet and triplet excited states, along with predictions of the singlets’ lifetimes. We illustrated these results using a Jablonski diagram that show the relative energy position of the singlet and longer-lived triplet excited states and analyzed and proposed relaxation paths for the excited state corresponding to the most intense but short-lived absorption (interconversion, intersystem crossing, fluorescence, and phosphorescence) that may lead to longer-lived excited states necessary for efficient charge separation required to generate current in solar cells.

14 SOLAR ENERGY↗

Modeling–Experiment–Theory Analysis of Reactions Initiated from Cl + Methyl Formate

Methyl formate (MF; CH 3 OCHO) is the smallest representative of esters, which are common components of biodiesel. The present study characterizes the thermal dissociation kinetics of the radicals formed by H atom abstraction from MF—CH 3 OCO and CH 2 OCHO—through a combination of modeling, experiment, and theory. For the experimental effort, excimer laser photolysis of Cl 2 was used as a source of Cl atoms to initiate reactions with MF in the gas phase. Time-resolved species profiles of MF, Cl 2 , HCl, CO 2 , CH 3 , CH 3 Cl, CH 2 O, and CH 2 ClOCHO were measured and quantified using photoionization mass spectrometry at temperatures of 400–750 K and 10 Torr. The experimental data were simulated using a kinetic model, which was informed by ab initio-based theoretical kinetics calculations and included chlorine chemistry and secondary reactions of radical decomposition products. Here, we calculated the rate coefficients for the H-abstraction reactions Cl + MF → HCl + CH 3 OCO (R1a) and Cl + MF → HCl + CH 2 OCHO (R1b): k 1a,theory = 6.71 × 10 –15 ·T 1.14 ·exp(—606/T) cm 3 /molecule·s; k 1b,theory = 4.67 × 10 –18 ·T 2.21 ·exp(—245/T) cm 3 /molecule·s over T = 200–2000 K. Electronic structure calculations indicate that the barriers to CH 3 OCO and CH 2 OCHO dissociation are 13.7 and 31.6 kcal/mol and lead to CH 3 + CO 2 (R3) and CH 2 O + HCO (R5), respectively. The master equation-based theoretical rate coefficients are k 3,theory (P = ∞) = 2.94 × 10 9 ·T 1.21 ·exp(—6209/T) s –1 and k 5,theory (P = ∞) = 8.45 × 10 8 ·T 1.39 ·exp(—15132/T) s –1 over T = 300–1500 K. The calculated branching fractions into R1a and R1b and the rate coefficient for R5 were validated by modeling of the experimental species time profiles and found to be in excellent agreement with theory. Additionally, we found that the bimolecular reactions CH 2 OCHO + Cl, CH 2 OCHO + Cl 2 , and CH 3 + Cl 2 were critical to accurately model the experimental data and constrain the kinetics of MF-radicals. Inclusion of the kinetic parameters determined in this study showed a significant impact on combustion simulations of larger methyl esters, which are considered as biodiesel surrogates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamic density functional theory of polymers with salt in electric fields

Here we present a dynamic density functional theory for modeling the effects of applied electric fields on the local structure of polymers with added salt (polymer electrolytes). Time-dependent equations for the local electrostatic potential and volume fractions of polymer, cation, and anion of added salt are developed using the principles of linear irreversible thermodynamics. For such a development, a field theoretic description of the free energy of polymer melts doped with salts is used, which captures the effects of local variations in the dielectric function. Connections of the dynamic density functional theory with experiments are established by relating the three phenomenological Onsager’s transport coefficients of the theory to the mutual diffusion of electrolyte, ionic conductivity, and transference number of one of the ions. The theory is connected with a statistical mechanical model developed by Bearman and Kirkwood [J. Chem. Phys. 28, 136 (1958)] after relating the three transport coefficients to friction coefficients. The steady-state limit of the dynamic density functional theory is used to understand the effects of dielectric inhomogeneity on the phase separation in polymer electrolytes. The theory developed here provides not only a way to connect with experiments but also to develop multi-scale models for studying connections between local structure and ion transport in polymer electrolytes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Beyond the Debye–Hückel limit: Toward a general theory for concentrated electrolytes

The phenomenon of underscreening in concentrated electrolyte solutions leads to a larger decay length of the charge–charge correlation than the prediction of Debye–Hückel (DH) theory and has found a resurgence of both theoretical and experimental interest in the chemical physics community. To systematically understand and investigate this phenomenon in electrolytes requires a theory of concentrated electrolytes to describe charge–charge correlations beyond the DH theory. We review the theories of electrolytes that can transition from the DH limit to concentrations where charge correlations dominate, giving rise to underscreening and the associated Kirkwood Transitions (KTs). In this perspective, we provide a conceptual approach to a theoretical formulation of electrolyte solutions that exploits the competition between molecular-informed short-range (SR) and long-range interactions. We demonstrate that all deviations from the DH limit for real electrolyte solutions can be expressed through a single function ΣQ that can be determined both theoretically and numerically. Importantly, ΣQ can be directly related to the details of SR interactions and, therefore, can be used as a tool to understand how differences in representations of interaction can influence collective effects. The precise function form of ΣQ can be inferred through a Gaussian field theory of both the number and charge densities. The resulting formulation is validated by experiment and can accurately describe the collective phenomenon of screening in concentrated bulk electrolytes. Importantly, the Gaussian field theory predictions of the screening lengths appear to be less than ∼1 nm at concentrations above KTs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Gauge-symmetrization method for energy-momentum tensors in high-order electromagnetic field theories

For electromagnetic field theories, canonical energy-momentum conservation laws can be derived from the underpinning spacetime translation symmetry according to the Noether procedure. However, the canonical energy-momentum tensors (EMTs) are neither symmetric nor gauge-symmetric (gauge invariant). The Belinfante-Rosenfeld (BR) method is a well-known procedure to symmetrize the EMTs, which also renders them gauge symmetric for first-order field theories. High-order electromagnetic field theories appear in the study of gyrokinetic systems for magnetized plasmas and the Podolsky system for the radiation reaction of classical charged particles. For these high-order field theories, gauge-symmetric EMTs are not necessarily symmetric and vice versa. In the present study, we develop a new gauge-symmetrization method for EMTs in high-order electromagnetic field theories. The Noether procedure is carried out using the Faraday tensor $F_{μν}$, instead of the 4-potential $A_{μ}$, to derive a canonical EMT $T^{μν}_{N}$. We show that the gauge-dependent part of $T^{μν}_{N}$ can be removed using the displacement-potential tensor $F^{σμν}$ ≡ $D^{σμ}A^{ν}/4π$, where $D^{σμ}$ is the antisymmetric electric displacement tensor. This method gauge-symmetrizes the EMT without necessarily making it symmetric, which is adequate for applications not involving general relativity. For first-order electromagnetic field theories, such as the standard Maxwell system, $F^{σμν}$ reduces to the familiar BR superpotential $S^{σμν}$, and the method developed can be used as a simpler procedure to calculate $S^{σμν}$ without employing the angular momentum tensor in 4D spacetime. When the electromagnetic system is coupled to classical charged particles, the gauge-symmetrization method for EMTs is shown to be effective as well.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Line operators in Chern-Simons-Matter theories and Bosonization in Three Dimensions II: Perturbative analysis and all-loop resummation

We study mesonic line operators in Chern-Simons theories with bosonic or fermionic matter in the fundamental representation. In this paper, we elaborate on the classification and properties of these operators using all loop resummation of large N perturbation theory. We show that these theories possess two conformal line operators in the fundamental representation. One is a stable renormalization group fixed point, while the other is unstable. They satisfy first-order chiral evolution equations, in which a smooth variation of the path is given by a factorized product of two mesonic line operators. The boundary operators on which the lines can end are classified by their conformal dimension and transverse spin, which we compute explicitly at finite ’t Hooft coupling. We match the operators in the bosonic and fermionic theories. Finally, we extend our findings to the mass deformed theories and discover that the duality still holds true.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗